A hands-on introduction to quarto with a Computo submission
May 23, 2024
Editorial board
IT support
Stat. learning, DR INRAE
Paris-Saclay University
Statistique, DR CNRS
IMT Toulouse
Optim./Machine-Learning
CR INRIA Lyon
CS/Stats/ML, IR CNRS
IMAG, Montpellier University
Machine learning, CR CNRS
Grenoble Alpes University
Statistics, MCF
Institut Agro Rennes-Angers
Machine Learning
CR MinesParisTech
Stats/ML/dev, IR CNRS
LBMC, ENS LYON
French statistical society appoints a “publication” commitee (lead by Julien then Pierre) to develop a new journal
Assessment
😔 Multiplication of “traditional” journals…
😔 No valorization of “negative” results
😥 No or not enough valorization of source codes and case studies
😱 ↘ of publication quality and time dedicated to each article (on author or reviewer sides) [1]
😱 Issue with scientific reproducibility (analyses, experiments) [2–7]
Point of view
⇝ Emergence of “Computo” idea
Scientific perimeter
Promote contribution in statistics and machine learning that provide insight into which models or methods are more appropriate to address a specific scientific question
Open access
⇝ In accordance with Budapest Open Access Initiative (BOAI) and Plan S
Reproducible
Official launch at the end of 2021
Notebook and literate programming
text (markdown) + math (\(\LaTeX\)) + code (Python/R/Julia), references (bib\(\TeX\))
Environment management, Compilation, Multi-format publication (pdf, html)
Continuous integration/Continuous deployment (CI/CD)
markdownRmarkdownPandocCredit: Pratik89Roy CC-BY-SA-4.0 from Wikimedia
with template notebook document + doc + pre-configured compilation and publication setup
Let’s go, locally (same spirit as Jupyter/Rmarkdown notebooks)
Configuration file versionned and used during CI compilation/publication action
A git push command will trigger your article compilation (including computations) and publication as a github page1
See the preconfigured .github/workflows/build.yml file for the github action configuration2
If the CI process succeeds, both HTML and PDF versions are published on the github-page associated to the repository
https://openreview.net/group?id=Computo
Submit:
After a “traditionnal” review process, a 3 step procedure:
including
🥲 Fully operational + doi, ISSN
🙂 7 published articles articles, 3 in preproduction, 6 under review (more details here)
🙂 x presentations (Montpellier, Toronto, Humastica, Grenoble, RR2023, etc.)
🙂 French reproducible research network
🤯 Difficult to find reviewers
🤔 Institutional support?
🤔 Changing of practices in the scientific community?
quarto: dynamic, agnostic language, FOSS1, community-based (pandoc), Rstudio/Posit supportgithub: dynamic, large user community but not institutional and limited computing resourcesQuarto is a new document format that is designed to make it easy to create, share, and publish reproducible research. In this workshop, we will learn how to use quarto to create a document that includes code, data, and narrative text. We will also learn how to submit our document to Computo.
To get started you will need to clone the mock repository for this workshop. You can do this by running the following command in your terminal:
Scientific and editorial reproducibility